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1.
Ann Oncol ; 35(2): 229-239, 2024 Feb.
Article in English | MEDLINE | ID: mdl-37992872

ABSTRACT

BACKGROUND: Increasingly, circulating tumor DNA (ctDNA) is proposed as a tool for minimal residual disease (MRD) assessment. Digital PCR (dPCR) offers low analysis costs and turnaround times of less than a day, making it ripe for clinical implementation. Here, we used tumor-informed dPCR for ctDNA detection in a large colorectal cancer (CRC) cohort to evaluate the potential for post-operative risk assessment and serial monitoring, and how the metastatic site may impact ctDNA detection. Additionally, we assessed how altering the ctDNA-calling algorithm could customize performance for different clinical settings. PATIENTS AND METHODS: Stage II-III CRC patients (N = 851) treated with a curative intent were recruited. Based on whole-exome sequencing on matched tumor and germline DNA, a mutational target was selected for dPCR analysis. Plasma samples (8 ml) were collected within 60 days after operation and-for a patient subset (n = 246)-every 3-4 months for up to 36 months. Single-target dPCR was used for ctDNA detection. RESULTS: Both post-operative and serial ctDNA detection were prognostic of recurrence [hazard ratio (HR) = 11.3, 95% confidence interval (CI) 7.8-16.4, P < 0.001; HR = 30.7, 95% CI 20.2-46.7, P < 0.001], with a cumulative ctDNA detection rate of 87% at the end of sample collection in recurrence patients. The ctDNA growth rate was prognostic of survival (HR = 2.6, 95% CI 1.5-4.4, P = 0.001). In recurrence patients, post-operative ctDNA detection was challenging for lung metastases (4/21 detected) and peritoneal metastases (2/10 detected). By modifying the cut-off for calling a sample ctDNA positive, we were able to adjust the sensitivity and specificity of our test for different clinical contexts. CONCLUSIONS: The presented results from 851 stage II-III CRC patients demonstrate that our personalized dPCR approach effectively detects MRD after operation and shows promise for serial ctDNA detection for recurrence surveillance. The ability to adjust sensitivity and specificity shows exciting potential to customize the ctDNA caller for specific clinical settings.


Subject(s)
Circulating Tumor DNA , Colorectal Neoplasms , Humans , Circulating Tumor DNA/genetics , DNA, Neoplasm/genetics , Algorithms , Colorectal Neoplasms/diagnosis , Colorectal Neoplasms/genetics , Denmark , Biomarkers, Tumor/genetics , Neoplasm Recurrence, Local
2.
Mol Biol Rep ; 49(2): 1609-1616, 2022 Feb.
Article in English | MEDLINE | ID: mdl-34811635

ABSTRACT

BACKGROUND: Mutational analysis of circulating tumor DNA (ctDNA) can potentially be used for early detection of recurrence after resection for hepatocellular carcinoma (HCC). Mutations from tumor may be identified in plasma as an early sign of recurrence. We conducted a pilot study investigating if somatic mutations could be detected in plasma in patients undergoing liver resection for HCC and in patients with advanced non-resectable HCC. METHODS AND RESULTS: We prospectively included patients undergoing curative liver resection for HCC. Tumor tissue was investigated with whole exome sequencing and preoperative blood samples were evaluated for ctDNA using targeted next-generation sequencing (NGS) with TruSight Oncology 500 including 523 cancer-associated genes. Subsequently, the method was evaluated in patients with advanced HCC. We included eight patients curatively resected for HCC, where tumor tissue mutations were identified in seven patients. However, only in one patient tumor specific mutations were found in the preoperative blood sample. In all three patients with advanced HCC, tumor mutations were detected in the blood. CONCLUSIONS: In patients with resectable HCC, ctDNA could not be reliably detected using the applied targeted NGS method. In contrast, ctDNA was detected in all patients with advanced HCC. Small tumors, tumor heterogeneity and limited sequencing coverage may explain the lack of detectable ctDNA.


Subject(s)
Carcinoma, Hepatocellular/genetics , Circulating Tumor DNA/genetics , Precision Medicine/methods , Aged , Aged, 80 and over , Biomarkers, Tumor/genetics , Carcinoma, Hepatocellular/diagnosis , Circulating Tumor DNA/analysis , DNA, Neoplasm/genetics , Denmark , Female , High-Throughput Nucleotide Sequencing/methods , Humans , Liver Neoplasms/diagnosis , Liver Neoplasms/genetics , Male , Middle Aged , Mutation , Pilot Projects , Exome Sequencing/methods
4.
Diabet Med ; 35(12): 1700-1706, 2018 12.
Article in English | MEDLINE | ID: mdl-29985535

ABSTRACT

AIMS: To investigate, in a large population in primary care, the relationship between fasting plasma glucose and HbA1c measurements, as well as the clinical implications of anaemia or chronic kidney disease for the interpretation of HbA1c values. METHODS: From a primary care resource, we examined HbA1c and fasting plasma glucose as well as haemoglobin and estimated GFR. We stratified observations by chronic kidney disease stage and anaemia level. The estimation of the mean fasting plasma glucose level from HbA1c alone, and from HbA1c , haemoglobin and estimated GFR, respectively, was evaluated. RESULTS: In 198 346 individuals, the fasting plasma glucose-HbA1c relationship mimicked the regression described in the A1c-Derived Average Glucose (ADAG) study, which was based on average capillary and interstitial glucose. The fasting plasma glucose-HbA1c relationship was unaffected in mild to moderate chronic kidney disease and in mild to moderate anaemia. The correlation changed only in severe hyperglycaemia and concurrent severe anaemia or when estimated GFR was <45 ml/min/1.73m², so that glucose concentration was underestimated by HbA1c in anaemia and overestimated in chronic kidney disease. The prevalence of estimated GFR <30 ml/min/1.73m² was 0.82%, while the prevalence of haemoglobin <81 g/l (5.0 mmol/l) was 0.11%. CONCLUSIONS: The relationship between fasting plasma glucose and HbA1c mimics that of the people with diabetes included in the ADAG study. Mild to moderate anaemia and CKD do not have a significant impact on the interpretation of HbA1c as a marker of retrograde glycaemia. Hence, it seems justified to use HbA1c without adjustment in primary care.


Subject(s)
Anemia/blood , Diabetes Mellitus, Type 2/blood , Glycated Hemoglobin/analysis , Primary Health Care , Renal Insufficiency, Chronic/blood , Adolescent , Adult , Aged , Aged, 80 and over , Anemia/complications , Anemia/epidemiology , Blood Glucose/analysis , Data Interpretation, Statistical , Databases as Topic , Denmark/epidemiology , Diabetes Complications/blood , Diabetes Complications/epidemiology , Diabetes Mellitus, Type 2/complications , Diabetes Mellitus, Type 2/epidemiology , Diagnostic Errors/statistics & numerical data , Female , General Practitioners/statistics & numerical data , Humans , Laboratories/statistics & numerical data , Male , Middle Aged , Practice Patterns, Physicians'/standards , Practice Patterns, Physicians'/statistics & numerical data , Primary Health Care/statistics & numerical data , Renal Insufficiency, Chronic/complications , Renal Insufficiency, Chronic/epidemiology , Young Adult
5.
J Intern Med ; 279(6): 566-75, 2016 06.
Article in English | MEDLINE | ID: mdl-26791682

ABSTRACT

BACKGROUND: Neutropenia, defined as an absolute blood neutrophil count (ANC) <1.5 G L(-1) , may accompany a variety of diseases. However, the clinical significance of neutropenia detected in a routine complete blood cell count is poorly understood. METHODS: Using a primary care resource, comprising more than 370 000 individuals, we assessed the association with a number of previously recognized conditions as well as all-cause mortality in the 4 years following the identification of neutropenia. By matching laboratory data with Danish nationwide health registers, risk estimates were assessed. RESULTS: Neutropenia was observed in approximately 1% of all individuals and was associated dose dependently with viral infections, haematological malignancies (but not autoimmune disorders or solid cancers) and mortality. Neutropenia was particularly associated with HIV, acute leukaemias and myelodysplastic syndromes. Odds ratios [95% confidence interval (CI)] for viral infections were 2.32 (1.84-2.91), 2.80 (2.20-3.57) and 4.77 (3.22-7.07) for subnormal (≥1.5-1.8 G L(-1) ), mild (≥1.0-1.5 G L(-1) ) and moderate-severe (≥0.0-1.0 G L(-1) ) neutropenic individuals, respectively (all P < 0.001). Likewise, odds ratios (95% CI) for haematological malignancies were 3.23 (2.35-4.45), 8.69 (6.58-11.47) and 46.03 (33.98-62.35 ), for the same neutropenia levels, respectively (all P < 0.001). Thus, the lower the ANC, the greater the likelihood of these diseases. The relative risk estimates observed for severe neutropenia corresponded to absolute risks of haematological malignancies and mortality from any cause of 40% and >50%, respectively. CONCLUSIONS: Neutropenia is an ominous sign necessitating careful follow-up. The risk estimates presented here support focusing attention to viral diseases and haematological malignancies when neutropenia is observed.


Subject(s)
Blood Cell Count , Hematologic Neoplasms/epidemiology , Neutropenia/epidemiology , Virus Diseases/epidemiology , Adolescent , Adult , Aged , Aged, 80 and over , Cause of Death , Child , Child, Preschool , Comorbidity , Female , Hematologic Neoplasms/immunology , Humans , Infant , Longitudinal Studies , Male , Middle Aged , Neutropenia/classification , Neutropenia/diagnosis , Prevalence , Prospective Studies , Registries , Risk Factors , Virus Diseases/immunology , Young Adult
6.
Br J Cancer ; 111(8): 1657-62, 2014 Oct 14.
Article in English | MEDLINE | ID: mdl-25117815

ABSTRACT

BACKGROUND: Genes with recurrent codon-specific somatic mutations are likely drivers of tumorigenesis and potential therapeutic targets. Hypermutable cancers may represent a sensitive system for generation and selection of oncogenic mutations. METHODS: We utilised exome-sequencing data on 25 sporadic microsatellite-instable (MSI) colorectal cancers (CRCs) and searched for base-specific somatic mutation hotspots. RESULTS: We identified novel mutation hotspots in 33 genes. Fourteen genes displayed mutations in the validation set of 254 MSI CRCs: ANTXR1, MORC2, CEP135, CRYBB1, GALNT9, KRT82, PI15, SLC36A1, CNTF, GLDC, MBTPS1, OR9Q2, R3HDM1 and TTPAL. A database search found examples of the hotspot mutations in multiple cancer types. CONCLUSIONS: This work reveals a variety of new recurrent candidate oncogene mutations to be further scrutinised as potential therapeutic targets.


Subject(s)
Mutation , Oncogenes , Humans , Microsatellite Instability , Neoplasms/genetics
7.
Cell Death Differ ; 20(11): 1485-97, 2013 Nov.
Article in English | MEDLINE | ID: mdl-23852374

ABSTRACT

Oncogenic stimuli trigger the DNA damage response (DDR) and induction of the alternative reading frame (ARF) tumor suppressor, both of which can activate the p53 pathway and provide intrinsic barriers to tumor progression. However, the respective timeframes and signal thresholds for ARF induction and DDR activation during tumorigenesis remain elusive. Here, these issues were addressed by analyses of mouse models of urinary bladder, colon, pancreatic and skin premalignant and malignant lesions. Consistently, ARF expression occurred at a later stage of tumor progression than activation of the DDR or p16(INK4A), a tumor-suppressor gene overlapping with ARF. Analogous results were obtained in several human clinical settings, including early and progressive lesions of the urinary bladder, head and neck, skin and pancreas. Mechanistic analyses of epithelial and fibroblast cell models exposed to various oncogenes showed that the delayed upregulation of ARF reflected a requirement for a higher, transcriptionally based threshold of oncogenic stress, elicited by at least two oncogenic 'hits', compared with lower activation threshold for DDR. We propose that relative to DDR activation, ARF provides a complementary and delayed barrier to tumor development, responding to more robust stimuli of escalating oncogenic overload.


Subject(s)
Carcinogenesis/genetics , DNA Damage , Neoplasms/genetics , Tumor Suppressor Protein p14ARF/genetics , Amino Acid Sequence , Animals , DNA-Binding Proteins/genetics , DNA-Binding Proteins/metabolism , Disease Models, Animal , Gene Expression , Heterografts , Humans , Immunohistochemistry , Mice , Molecular Sequence Data , Neoplasms/metabolism , Neoplasms/pathology , Oncogenes , Transfection , Tumor Suppressor Protein p14ARF/metabolism
8.
Oncogene ; 31(40): 4409-19, 2012 Oct 04.
Article in English | MEDLINE | ID: mdl-22249255

ABSTRACT

Loss of tumour suppressor gene function can occur as a result of epigenetic silencing of large chromosomal regions, referred to as long-range epigenetic silencing (LRES), and genome-wide analyses have revealed that LRES is present in many cancer types. Here we utilize Illumina Beadchip methylation array analysis to identify LRES across 800 kb of chromosome 5q31 in colorectal adenomas and carcinomas (n=34) relative to normal colonic epithelial DNA (n=6). This region encompasses 53 individual protocadherin (PCDH) genes divided among three gene clusters. Hypermethylation within these gene clusters is asynchronous; while most PCDH hypermethylation occurs early, and is apparent in adenomas, PCDHGC3 promoter methylation occurs later in the adenoma-carcinoma transition. PCDHGC3 was hypermethylated in 17/28 carcinomas (60.7%) according to methylation array analysis. Quantitative real-time reverse transcription-polymerase chain reaction showed that PCDHGC3 is the highest expressed PCDH in normal colonic epithelium, and that there was a strong reciprocal relationship between PCDHGC3 methylation and expression in carcinomas (R=-0.84). PCDH LRES patterns are reflected in colorectal tumour cell lines; adenoma cell lines are not methylated at PCDHGC3 and show abundant expression at the mRNA and protein level, while the expression is suppressed in hypermethylated carcinoma cell lines (R=-0.73). Short-interfering RNA-mediated reduction of PCDHGC3 led to a decrease of apoptosis in RG/C2 adenoma cells, and overexpression of PCDHGC3 in HCT116 cells resulted in the reduction of colony formation, consistent with tumour suppressor capabilities for PCDHGC3. Further functional analysis showed that PCDHGC3 can suppress Wnt and mammalian target of rapamycin signalling in colorectal cancer cell lines. Taken together, our data suggest that the PCDH LRES is an important tumour suppressor locus in colorectal cancer, and that PCDHGC3 may be a strong marker and driver for the adenoma-carcinoma transition.


Subject(s)
Cadherins/genetics , Chromosomes, Human, Pair 5 , Colorectal Neoplasms/genetics , Epigenesis, Genetic , Gene Silencing , Cadherin Related Proteins , Cell Transformation, Neoplastic/genetics , Gene Expression Regulation, Neoplastic , HCT116 Cells , Humans , Signal Transduction/genetics
9.
Oncogene ; 31(22): 2750-60, 2012 May 31.
Article in English | MEDLINE | ID: mdl-21963845

ABSTRACT

Aberrant activation of the Wnt signaling pathway is causally involved in the formation of most colorectal cancers (CRCs). Although detailed knowledge exists regarding Wnt-regulated protein-coding genes, much less is known about the possible involvement of non-coding RNAs. Here we used TaqMan Array MicroRNA Cards, capable of detecting 664 unique human microRNAs (miRNAs), to describe changes of the miRNA transcriptome following disruption of beta-catenin/TCF4 activity in DLD1 CRC cells. Most miRNAs appeared to respond independent of host gene regulation and proximal TCF4 chromatin occupancy as inferred from expression microarray and ChIP-chip data. A module of miRNAs induced by abrogated Wnt signaling in vitro was downregulated in two independent series of human primary CRCs (n=76) relative to normal adjacent mucosa (n=34). Several of these miRNAs (miR-145, miR-126, miR-30e-3p and miR-139-5p) markedly inhibited CRC cell growth in vitro when ectopically expressed. By using an integrative approach of proteomics and expression microarrays, we found numerous mRNAs and proteins to be affected by ectopic miR-30e-3p levels. This included HELZ and PIK3C2A that were directly repressed by several miRNA binding sites as confirmed by luciferase reporter assays in combination with mutational analyses. Finally, small interfering RNA-mediated downregulation of PIK3C2A, but not HELZ, was sufficient on its own to restrict CRC cell growth. Collectively, our study demonstrates that multiple miRNAs are upregulated as a consequence of forced attenuation of Wnt signaling in CRC cells, and some of these miRNAs inhibit cell growth with concomitant suppression of several growth-stimulatory cancer-related genes.


Subject(s)
Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/metabolism , Colorectal Neoplasms/genetics , Colorectal Neoplasms/pathology , MicroRNAs/genetics , Oncogenes/physiology , Transcription Factors/metabolism , Transcriptome , beta Catenin/metabolism , Aged , Aged, 80 and over , Basic Helix-Loop-Helix Leucine Zipper Transcription Factors/genetics , Cell Line, Tumor , Cell Proliferation , Chromatography, Liquid , Colon/metabolism , Colorectal Neoplasms/metabolism , Female , Gene Expression Profiling , Genes, Dominant , Humans , Luciferases/metabolism , Male , Middle Aged , Oligonucleotide Array Sequence Analysis , RNA, Messenger/genetics , RNA, Small Interfering , Rectum/metabolism , Reverse Transcriptase Polymerase Chain Reaction , Spectrometry, Mass, Matrix-Assisted Laser Desorption-Ionization , Transcription Factor 4 , Transcription Factors/genetics , Tumor Cells, Cultured , Wnt Signaling Pathway , beta Catenin/genetics
10.
Br J Cancer ; 105(4): 552-61, 2011 Aug 09.
Article in English | MEDLINE | ID: mdl-21772334

ABSTRACT

BACKGROUND: The KIAA1199 transcript is upregulated in colon adenomas and downregulated upon ß-catenin knockdown. METHODS: Transcript profiling was performed on >500 colon biopsies, methylation profiling data were compared with transcript data. Immunohistochemistry assessed KIAA1199 protein expression in 270 stage II/III tumours (>3 years follow-up). The effects of stable KIAA1199 knockdown in SW480 cells (three different constructs) were studied using transcriptional profiling, proliferation and protein analysis. RESULTS: The KIAA1199 transcript was strongly upregulated in 95% of adenocarcinomas. Absent expression in normal mucosa correlated with KIAA1199 promotor methylation. Nuclear and cytoplasmic KIAA1199 protein expression was identified in colon adenocarcinomas and other types of cancers. A subpopulation of patients with tumours strongly expressing KIAA1199 in the nucleus showed a better outcome with regard to recurrence as lung or liver metastases. The KIAA1199 knockdown affected the cell cycle and the Wnt-signalling pathway. Reduced cellular proliferation and decreased KI67, phosphorylated retinoblastoma, ß-catenin and ASCL2 protein expression supported these findings. Eighteen Wnt-signalling genes differentially expressed upon KIAA1199 knockdown correlated with the KIAA1199 expression profile in clinical specimens. CONCLUSION: The KIAA1199 knockdown attenuates the effects of the Wnt/ß-catenin signalling and it may thus be regarded as a regulatory part of this pathway.


Subject(s)
Adenocarcinoma/metabolism , Adenocarcinoma/pathology , Colorectal Neoplasms/metabolism , Colorectal Neoplasms/pathology , Proteins/metabolism , Signal Transduction , Wnt Proteins/metabolism , Cell Adhesion , Cell Movement , Cell Proliferation , Gene Expression Regulation, Neoplastic , Humans , Hyaluronoglucosaminidase , Immunohistochemistry , Microscopy, Fluorescence , Neoplasm Staging , Protein Array Analysis , Proteins/genetics , Up-Regulation
11.
Br J Cancer ; 100(3): 511-23, 2009 Feb 10.
Article in English | MEDLINE | ID: mdl-19156145

ABSTRACT

The aim of this study was to identify deregulated transcription factors (TFs) in colorectal cancer (CRC) and to evaluate their relation with the recurrence of stage II CRC and overall survival. Microarray-based transcript profiles of 20 normal mucosas and 424 CRC samples were used to identify 51 TFs displaying differential transcript levels between normal mucosa and CRC. For a subset of these we provide in vitro evidence that deregulation of the Wnt signalling pathway can lead to the alterations observed in tissues. Furthermore, in two independent cohorts of microsatellite-stable stage II cancers we found that high SOX4 transcript levels correlated with recurrence (HR 2.7; 95% CI, 1.2-6.0; P=0.01). Analyses of approximately 1000 stage I-III adenocarcinomas, by immunohistochemistry, revealed that patients with tumours displaying high levels of CBFB and SMARCC1 proteins had a significantly better overall survival rate (P=0.0001 and P=0.0275, respectively) than patients with low levels. Multivariate analyses revealed that a high CBFB protein level was an independent predictor of survival. In conclusion, several of the identified TFs seem to be involved in the progression of CRC.


Subject(s)
Colorectal Neoplasms/genetics , Core Binding Factor beta Subunit/genetics , SOXC Transcription Factors/genetics , Transcription Factors/genetics , Adult , Aged , Aged, 80 and over , Cell Line, Tumor , Colorectal Neoplasms/pathology , Female , Humans , Immunohistochemistry , Male , Microsatellite Repeats/genetics , Middle Aged , RNA, Messenger/genetics , Reverse Transcriptase Polymerase Chain Reaction , Survival Analysis
12.
Histol Histopathol ; 23(9): 1069-76, 2008 09.
Article in English | MEDLINE | ID: mdl-18581278

ABSTRACT

BACKGROUND: The identification of new prognostic markers in prostate cancer (PC) is essential to improve patient treatment and management. Data suggest that SMARCC1 protein, a part of the intranuclear SWI/SNF complex which enhances the transactivation of the androgen receptor, is upregulated in PC and therefore a possible candidate marker for PC progression. MATERIALS: Expression of SMARCC1 immunostaining was analysed on a tissue microarray containing specimens from 327 patients with prostate cancer and clinical follow-up information. Furthermore, 30 specimens from patients with benign prostate hyperplasia were included as controls as well as 30 specimens of benign prostate tissue from PC patients. Also, 18 specimens from lymph node metastases were analysed. RESULTS: All benign specimens showed no or minimal staining for SMARCC1. In contrast, 20% of the specimens from patients with non-metastatic and non-recurrent disease showed moderate to marked staining. In 31% of the patients with recurrent disease and in 31% of the patients with metastatic disease we found moderate to strong SMARCC1 immunostaining. In total, 23% of lymph node metastases expressed SMARCC1. SMARCC1 expression was also positively correlated to Gleason score (p<0.05), clinical T stage (p<0.01) and time to recurrence (p<0.001). In a logistic regression analysis, patients with a marked SMARCC1 immunostaining had a significantly elevated odds ratio (OR) of 16 for recurrent cancer and an OR of 4.5 for metastatic disease. Conclusions. Our present results demonstrate an increased expression of SMARCC1 protein in prostate cancer and reveal a positive correlation with tumour dedifferentiation, progression, metastasis and time to recurrence.


Subject(s)
Adenocarcinoma/metabolism , Prostatic Neoplasms/metabolism , Transcription Factors/metabolism , Adenocarcinoma/secondary , Adenocarcinoma/surgery , Animals , Biomarkers, Tumor/metabolism , COS Cells , Cell Dedifferentiation , Cell Nucleus/metabolism , Cell Nucleus/pathology , Chlorocebus aethiops , Fluorescent Antibody Technique, Direct , Humans , Immunoenzyme Techniques , Lymph Nodes/metabolism , Lymph Nodes/pathology , Lymphatic Metastasis , Male , Neoplasm Recurrence, Local , Odds Ratio , Prostate/metabolism , Prostate/pathology , Prostatic Hyperplasia/metabolism , Prostatic Hyperplasia/pathology , Prostatic Neoplasms/pathology , Prostatic Neoplasms/surgery , Tissue Array Analysis , Up-Regulation
13.
Br J Cancer ; 96(12): 1896-903, 2007 Jun 18.
Article in English | MEDLINE | ID: mdl-17519897

ABSTRACT

Microarray analysis on pooled samples has previously identified ZDHHC9 (DHHC9) to be upregulated in colon adenocarcinoma compared to normal colon mucosa. Analyses of 168 samples from proximal and distal adenocarcinomas using U133plus2.0 microarrays validated these findings, showing a significant two-fold (log 2) upregulation of DHHC9 transcript (P<10(-6)). The upregulation was more striking in microsatellite stable (MSS), than in microsatellite instable (MSI), tumours. Genes known to interact with DHHC9 as H-Ras or N-Ras did not show expression differences between MSS and MSI. Immunohistochemical analysis was performed on 60 colon adenocarcinomas, previously analysed on microarrays, as well as on tissue microarrays with 40 stage I-IV tumours and 46 tumours from different organ sites. DHHC9 protein was strongly expressed in MSS compared to MSI tumours, readily detectable in premalignant lesions, compared to the rare expression seen in normal mucosa. DHHC9 was specific for tumours of the gastrointestinal tract and localised to the Golgi apparatus, in vitro and in vivo. Overexpression of DHHC9 decreased the proliferation of SW480 and CaCo2 MSS cell lines significantly. In conclusion, DHHC9 is a gastrointestinal-related protein highly expressed in MSS colon tumours. The palmitoyl transferase activity, modifying N-Ras and H-Ras, suggests DHHC9 as a target for anticancer drug design.


Subject(s)
Acyltransferases/genetics , Colorectal Neoplasms/genetics , Cell Division , Colonic Neoplasms/genetics , Colonic Neoplasms/pathology , Colorectal Neoplasms/classification , Colorectal Neoplasms/pathology , DNA, Neoplasm/genetics , Gene Expression Regulation, Neoplastic , Humans , Intestinal Mucosa/cytology , Microsatellite Repeats/genetics , Nucleic Acid Hybridization , Oligonucleotide Array Sequence Analysis , Plasmids , RNA, Neoplasm/genetics , Rectal Neoplasms/genetics , Rectal Neoplasms/pathology , Zinc Fingers/genetics
14.
Br J Cancer ; 96(3): 499-506, 2007 Feb 12.
Article in English | MEDLINE | ID: mdl-17245344

ABSTRACT

Prostate cancer (PCa) is the most commonly diagnosed non-cutaneous cancer in male subjects in Western countries. The widespread use of prostate-specific antigen (PSA) has increased the detection of this cancer form in earlier stages. Moreover, it has increased the need for new diagnostic procedures to be developed for patient stratification based on risk of progression. We analysed laser-microdissected prostate tumour tissue from 43 patients with histologically verified PCa, using the new high-resolution Affymetrix Mapping 50K single-nucleotide polymorphism array. The results showed six major loss of heterozygosity regions at chromosomes 6q14-16, 8p23-11, 10q23, 13q13-21 and 16q21-24 and a novel region at chromosome 21q22.2, all of which reveal concomitant copy number loss. Tumour development was further characterised by numerous novel genomic regions almost exclusively showing copy number loss. However, tumour progression towards a metastatic stage, as well as poor differentiation, was identified by specific patterns of copy number gains of genomic regions located at chromosomes 8q, 1q, 3q and 7q. Androgen ablation therapy was further characterised by copy gain at chromosomes 2p and 10q. In conclusion, patterns of allelic imbalance were discovered in PCa, consisting allelic loss as an early event in tumour development, and distinct patterns of allelic amplification related to tumour progression and poor differentiation.


Subject(s)
Allelic Imbalance , Oligonucleotide Array Sequence Analysis/methods , Polymorphism, Single Nucleotide , Prostatic Neoplasms/genetics , DNA, Neoplasm/analysis , Gene Dosage , Genome, Human , Genotype , Humans , Loss of Heterozygosity , Male , Prostatic Neoplasms/pathology
15.
Br J Cancer ; 95(10): 1415-8, 2006 Nov 20.
Article in English | MEDLINE | ID: mdl-17003783

ABSTRACT

We report on the location of 283 miRNAs in the human genome in relation to copy number changes in three distinct types of tumours: prostate, bladder and colon. In prostate and colon tumours, we find miRNAs over-represented in regions with copy number gain and under-represented in regions with copy number loss. Surprisingly this pattern appears to be reversed in bladder cancer. We compared our miRNA copy number data to published miRNA expression data; unexpectedly, we did not find a statistically significant relationship between miRNA copy number and expression level. This suggests that miRNA expression is regulated through different mechanisms than mRNA expression.


Subject(s)
Genome, Human , MicroRNAs/genetics , Neoplasms/genetics , Colonic Neoplasms/pathology , Gene Dosage , Gene Expression Profiling , Humans , Male , Neoplasms/pathology , Nucleic Acid Hybridization/methods , Oligonucleotide Array Sequence Analysis , Prostatic Neoplasms/pathology , Urinary Bladder Neoplasms/genetics
16.
J Econ Entomol ; 99(3): 803-10, 2006 Jun.
Article in English | MEDLINE | ID: mdl-16813315

ABSTRACT

The flea beetles Phyllotreta cruciferae (Goeze) and Phyllotreta striolata (F.) (Coleoptera: Chrysomelidae: Alticinae) are significant pests of crops in the Brassicaceae family. From 2001 to 2003, the efficacy of both new and commonly used treatments for the control of flea beetles in brassicas, Brassica rapa L., were evaluated in three small plot, randomized complete block design trials. Row cover and carbaryl (applied as a weekly foliar spray) were found to be the most consistent at reducing damage in comparison with untreated controls in all trials. Two new products that may provide adequate flea beetle control are spinosad (in either conventional or organic formulations) and thiamethoxam. The plant-derived compounds azidiractin and pyrethrin did not protect treated plants from flea beetle feeding. Treatment of plants with kaolin, or removal of the beetles with a vacuum, also did not reduce the level of crop damage. The level of damage at harvest was found to be correlated with population size of flea beetles in each plot, as measured by captures on yellow sticky traps and direct visual counts. Removal of the outer two leaves of individual B. rapa plants reduced the total number of holes per plant by 40%, while only removing 15% of the leaf area.


Subject(s)
Brassica rapa/parasitology , Coleoptera , Pest Control/methods , Agriculture/methods , Animals , Food, Organic , Insecticides , Massachusetts
17.
Biochim Biophys Acta ; 1758(10): 1587-95, 2006 Oct.
Article in English | MEDLINE | ID: mdl-16836975

ABSTRACT

Verapamil is used clinically as a Ca(2+) channel inhibitor for the treatment of various disorders such as angina, hypertension and cardiac arrhythmia. Here we study the effect of verapamil on the bacterium Escherichia coli. The drug was shown to inhibit cell division at growth sub inhibitory concentrations, independently of the SOS response. We show verapamil is a membrane active drug, with similar effects to dibucaine, a local anesthetic. Thus, both verapamil and dibucaine abolish the proton motive force and decrease the intracellular ATP concentration. This is accompanied by induction of degP expression, as a result of the activation of the RpoE (SigmaE) extra-cytoplasmic stress response, and activation of the psp operon. Such effects of verapamil, as a membrane active compound, could explain its general toxicity in eukaryotic cells.


Subject(s)
Calcium Channel Blockers/pharmacology , Escherichia coli/drug effects , Sigma Factor/biosynthesis , Transcription Factors/biosynthesis , Verapamil/pharmacology , Anesthetics, Local/pharmacology , Bacterial Proteins/biosynthesis , Bacterial Proteins/genetics , Dibucaine/pharmacology , Escherichia coli/genetics , Escherichia coli Proteins/biosynthesis , Heat-Shock Proteins/biosynthesis , Membrane Potentials/drug effects , Periplasmic Proteins/biosynthesis , Serine Endopeptidases/biosynthesis
18.
Br J Cancer ; 92(12): 2240-8, 2005 Jun 20.
Article in English | MEDLINE | ID: mdl-15956967

ABSTRACT

The majority of microsatellite instable (MSI) colorectal cancers are sporadic, but a subset belongs to the syndrome hereditary non-polyposis colorectal cancer (HNPCC). Microsatellite instability is caused by dysfunction of the mismatch repair (MMR) system that leads to a mutator phenotype, and MSI is correlated to prognosis and response to chemotherapy. Gene expression signatures as predictive markers are being developed for many cancers, and the identification of a signature for MMR deficiency would be of interest both clinically and biologically. To address this issue, we profiled the gene expression of 101 stage II and III colorectal cancers (34 MSI, 67 microsatellite stable (MSS)) using high-density oligonucleotide microarrays. From these data, we constructed a nine-gene signature capable of separating the mismatch repair proficient and deficient tumours. Subsequently, we demonstrated the robustness of the signature by transferring it to a real-time RT-PCR platform. Using this platform, the signature was validated on an independent test set consisting of 47 tumours (10 MSI, 37 MSS), of which 45 were correctly classified. In a second step, we constructed a signature capable of separating MMR-deficient tumours into sporadic MSI and HNPCC cases, and validated this by a mathematical cross-validation approach. The demonstration that this two-step classification approach can identify MSI as well as HNPCC cases merits further gene expression studies to identify prognostic signatures.


Subject(s)
Adenocarcinoma/genetics , Colonic Neoplasms/genetics , Colorectal Neoplasms, Hereditary Nonpolyposis/genetics , Gene Expression/genetics , Adult , Aged , Aged, 80 and over , Base Pair Mismatch/genetics , Chromosomal Instability/genetics , DNA Repair/genetics , Gene Expression Profiling , Humans , Microsatellite Repeats/genetics , Middle Aged , Oligonucleotide Array Sequence Analysis , Predictive Value of Tests
19.
Cytometry ; 45(2): 83-6, 2001 Oct 01.
Article in English | MEDLINE | ID: mdl-11590619

ABSTRACT

BACKGROUND: The recently developed tissue microarray (TMA) technology allows the arrangement of up to a thousand tissue specimens on a single microscope slide. This technology enables researchers to perform gene copy number studies on very large series of archival formalin-fixed tissues using fluorescence in situ hybridization (FISH). However, the hybridization properties of individual archival specimens can vary considerably. Therefore a highly optimized protocol is needed to fulfill the task of producing evaluable hybridization signals simultaneously in hundreds of specimens in a TMA. METHODS: The performance of two different FISH protocols, the standard protocol for paraffin embedded tissues and our new optimized protocol, was tested on TMAs using probes for the HER-2 and ZNF217 genes as well as the chromosome 17 centromere. RESULTS: The new protocol resulted in greatly increased signal intensity and an almost 30% increase in the number of tissue samples with evaluable hybridization signals. CONCLUSIONS: Our improved protocol for FISH on TMAs provides standardized hybridization conditions leading to high-quality hybridization signals in the majority of specimens. The increases in the signal intensity and the number of evaluable samples are extremely important for the successful analyses of TMAs by FISH and will allow the utilization of the TMA technology in its full potential.


Subject(s)
Autoantigens , Breast Neoplasms/genetics , Gene Amplification , Gene Dosage , In Situ Hybridization, Fluorescence/methods , Breast/pathology , Breast Neoplasms/pathology , Centromere Protein A , Chromosomal Proteins, Non-Histone/genetics , Female , Humans , Paraffin Embedding , Receptor, ErbB-2/genetics , Trans-Activators/genetics
20.
Ann Allergy Asthma Immunol ; 84(5): 509-16, 2000 May.
Article in English | MEDLINE | ID: mdl-10831004

ABSTRACT

BACKGROUND: Although asthma clinical pathways are used with increasing frequency, few controlled studies have evaluated the clinical and cost effectiveness of these pathways. OBJECTIVE: To evaluate the effect of an inpatient asthma clinical pathway on cost and quality of care for children with asthma. METHODS: One hundred forty-nine children were treated for status asthmaticus using an asthma clinical pathway in a children's hospital between September and December 1997. Thirty-four of 149 children treated with the clinical pathway were randomly selected. A retrospective cohort control group of non-pathway patients (N = 34) was matched with each pathway patient by age, race, gender, co-morbidities, asthma severity score, ICU admission, and time of year admitted. Differences between the two groups in length of stay, total costs, readmission rate, inpatient management, and discharge medications were compared. RESULTS: Length of stay was significantly lower in the clinical pathway group compared with the control group (36 hours versus 71 hours, P < .001) and total costs decreased significantly ($1685 versus $2829, P < .001) as a result of the pathway. Asthmatic children on the clinical pathway were significantly more likely than the control group to complete asthma teaching while hospitalized (65% versus 18%, P < .001), to be discharged with a prescription for a controller medication (88% versus 53%, P < .01), and to have a peak flow meter (57% versus 23%, P < .05) and a spacer device (100% versus 71%, P < .001) for home use. CONCLUSION: Implementation of this inpatient clinical pathway led to a decrease in length of stay and a reduction in total cost while improving quality of care for hospitalized asthmatic children.


Subject(s)
Asthma/therapy , Hospitalization , Child , Child, Preschool , Costs and Cost Analysis , Humans , Length of Stay/economics , Patient Care Team/standards , Patient Education as Topic , Treatment Outcome
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